Chuck vs The Shadows of Orion
by SilentRevelation
Summary: With the passing of his Father Chuck must assume a heavy burden. But is Chuck ready to face the unspeakable terrors that Orion has been keeping at bay for all of these years? Team Bartowski must be ready to face their deadliest foe to date. Possible S4.


**Chuck Vs. The Shadows of Orion  
**

**A/N** I am in no way an author, an artist or an owner of Chuck. This is my 2nd attempt at FanFiction but it really should be my first seeing as how my first attempt crashed and burned. I was a terrible writer who has now hopefully improved (at least marginally).

I have two stories currently in the works and have actually been having a lot of trouble deciding upon which I want to publish, so I'm depending on you, the wonderful people to help me decide. If this story receives a good response than I will most certainly continue it, if it does not than I can safely leave it as a one shot. So please leave me feedback if you enjoyed this chapter and want to see more. I would like to thank all of you in advance for taking time out of your busy schedule to read my lowly fanfic. Thank you!

**Brief Synopsis:** This story picks up where S3 ended and can hopefully act as a plausible Season 4 substitute until we can receive the real thing. I can't give away much more without spoiling it. Thank you! 

**Chapter 1 – It is too soon to act.  
**

"Mom?" Chuck's eyes glazed over as he squeezed the half piece of charm that remained from his mother's necklace. The cool metal warmed and cut into his skin as he clenched the necklace in his fist and the fresh Flash washed over him.

_Roses  
Tron movie poster_

Marriage certificate issued by the state of California for Stephen and Mary Bartowski.

Pictures of a young Ellie and Chuck building sand castles on the beach with a middle aged brunette woman.

Missing person's police reports.

An evidence bag containing a short silver dagger with a crescent moon surrounded by three stars etched into its ivory handle.

A world map with dozens of pegged locations and notations.

A letter dated March 13, 1992 written by Stephen Bartowski to a woman named Elizabeth Swanson begging her to return home to her children. Her only response was, "Not until it's finished."

Tron movie poster  
Roses

_ "_Whoa!" Chuck exclaimed while silently shaking the affects of the large flash out of his head. Stunned, Chuck couldn't help but stare at the piece of his mother's charm and its bloody outline now etched into his hand. Chuck took in all of his surroundings: Stacks of file boxes, trinkets and broken instruments lined the 10ft high warehouse shelving that took up the majority of Orion's underground lair. The large sub-basement's concrete floors and walls were dimly lit and the air was cool and dry, perfect conditions for the large control consoles and PC's that popped up intermittently.

_Where did Dad get the funding for all of this and how was he able to keep this a secret? This place is bigger than Castle, or what used to be Castle._ Chuck thought sadly as he examined the files near his father's desk, one in particular caught his attention.

_Mary Elizabeth Bartowski: Missing_

_I'm just not ready to look at that file yet. Dad has everything here though, the walls are lined with thousands of files on criminals and missing persons I've never even heard of. Why though? Why was he doing all of this? Could this all really have been to protect Ellie and me? _Chuck considered these questions as he pulled a file box down from an eye level shelf and blew dust off of the lid. "_Hydra," who or what is Hydra? _Chuck pondered as he opened the box and pulled out the first file. It contained photos of bank vaults, armored trucks and even government facilities, all seemingly random targets sharing important similarities. Each building, vault and truck had been neatly cut into in obscure places, robbed, and then flooded it seems.

Chuck considered the possibilities of these crimes until he reached the final photo in the stack; the picture of a young girl who had been brutally disfigured and murdered. The flash hit him before he could look away.

_A submarine.  
An original yellow Super Soaker 1500._

Schematics for a prototype high pressure tank as well as a formula for expanding water molecules.

Grainy Video footage of a bank lobby with a young brunette girl - around the age of six - standing in line at the bank and holding the hand of an older woman. A man whom appeared to be dressed as a scuba diver in body armor stepped into frame and demanded that everyone get down on the ground. The man then proceeded to reach behind him and turn on the massive tank strapped to his bank. He then struck a Spiderman-esque pose and threw his arms out in front of himself as super-powered thin jets of water shot from hoses under his wrist. The jets of water began deeply cutting into anything and everyone in his path with merciless and ruthless force. Unfortunately the small girl was caught in the blast before the armored man could turn his attention to the surveillance camera. The video went black.

Reports filed by the FBI that contained a list of deceased, monies and technology stolen and stamped "whereabouts unknown."

An original yellow Super Soaker 1500  
A submarine.

Chuck had seen some terrible things during his brief career with the CIA but none would ever haunt him as much as the photo of the murdered young girl and the masked figure who took her life. Just as Chuck managed to put the file back into place and reach up to wipe the tears off of his cheek the perimeter alarms went off.

Red caution lights and sirens began to illuminate Orion's concrete bunker as Chuck rushed to the nearest console filled with surveillance footage. The urgency was for not as Chuck took in the breath taking image of Sarah Walker stealthily entering the living room of Chuck's childhood home. She had obviously followed him straight here as she was still dressed from their family dinner earlier.

_I guess she didn't really believe me when I said I was going to go pick up a couple of items that my father had left Ellie and I. It wasn't really a lie. _Chuck just shook his head as he considered his possibilities in this scenario. Tired of lying to the woman of his dreams he headed back towards the staircase that led him to the fireplace and his waiting girlfriend.

Sarah was still investigating the living room and kitchen when the fireplace began receding into the wall allowing Chuck entrance back into the living room. Chuck's head poked up from the floor to find a very angry looking Sarah Walker looking down at him with her hands placed on her hips and her gun noticeably sticking out from the waist of her skirt.

Frustrated, Sarah blew the misplaced bangs out of her line of vision and uttered just one word to Chuck, "Explain."

Chuck couldn't help but gulp a little as Sarah stared him down with that determined look in her eyes. A look he was certain had broken numerous Russian Counter-Intelligence agents and more than a few Columbian Drug Dealers. "Well Sweetie, you look very beautiful tonight, did I tell you that earlier? Also, you know that I love you very mu…"

"Chuck, explain." Sarah said raising her voice and cutting Chuck off as she reached one hand around and casually tapped the handle of her Sig Sauer with her index finger.

Chuck let out a second audible gulp. "Okay, no more stalling, lies or omissions. My dad left me a message and said that I needed to come here tonight and come here alone. He said that he was sorry but that he had left me a job to do, a very important one. Well, come on Sarah, you'll just have to come down here and see for yourself." Chuck motioned for Sarah to join him on the hidden staircase and then held his hand out for her to hold onto. Sarah glanced down at Chuck's hand, ignored it and then gracefully slipped past him.

Chuck then found Sarah standing at the bottom of the stairs looking in wonder at the several hundred yards of underground warehouse and thousands of file boxes that adorned the shelves. "What the… Chuck? Explain." Sarah said dazedly as she lightly leaned against the concrete wall for support.

"So Sarah, apparently my dad has been keeping himself very busy over the last 20 years. In his message he said that he'd been a spy, and he's been working for himself trying to keep the world's most notorious criminals at bay as well as keeping them off of Ellie and I's trail. But his message said that now that he's gone we might be in trouble."

"What else is new?" Was all Sarah could say as she leaned further against the wall and continued to take in the entire expanse of Orion's lair.

"Sarah! You've got to see it; he's got thousands of files on criminals, rows and rows of weapons and gadgets, and Computers… Oh Sarah you've got to see the computers!" Chuck grabbed Sarah by the wrist and led her along the center isle; alarm beams rising as they neared.

"Chuck, what does all of this mean though? You told Ellie that you were quitting the CIA and that you were done with being a spy." Sarah couldn't help but frown as the last few words crossed her lips, but Chuck didn't seem to notice.

"Sarah you don't understand, I did quit, and you know that I contacted Beckman earlier today and gave her my resignation. This is all too big though Sarah; I can't turn my back on all of this, especially if it's going to bring even more danger to Ellie and Devon. I promise I will tell Ellie soon and explain to her why I have to do this. She'll understand, especially when I show her this." Chuck pointed to the box labeled: "Mary Elizabeth Bartowski: Missing."

"Chuck, is that- is that your mother? Have you already looked inside?"

"No, I couldn't do it alone because I don't know what I would find. I did flash on a charm necklace that she kept though and it showed me a list of known locations, aliases and a missing persons report." Chuck grimaced and looked at Sarah

Sarah returned Chuck's look with a sympathetic smile, "that's one thing that I've always thought we had in common, because you know I don't know where my mother is either. So, I understand how important it is for you to find her. Whenever you're ready I promise to be there with you when you open that box." Sarah moved in closer and hugged Chuck close. They both stood there embraced for several moments; Sarah listening to Chuck's heart beat and Chuck taking in the vanilla scent of Sarah's shampoo.

Sarah was the first to pull away; "whatever you want to do, with all of this," she said motioning to their dusty surroundings, "I will support you. But let's not decide tonight, it's too soon. We need to let everything from today sink in first." Smiling sadly, Sarah reached up with both hands and pulled Chuck down to her for a thoughtful and loving kiss.

Chuck sighed, "I know, I just don't think Ellie is going to share that sentiment."

****

Casa Bartowski.  
Chuck and Sarah's bedroom.  
May 25, 2010. 2:30 am.

Chuck couldn't sleep. It was as simple as that. He and Sarah had remained at his old family home for a few more minutes examining old files before Sarah suggested they go home and sleep on their decision. Now Chuck couldn't sleep, he simply had too many things going on in his head to find the clarity a good night's rest would bring. Every time he closes his eyes he sees his father falling backwards, he hears his final words and watches his eyes glaze over as his last breath escapes him. But he doesn't have time to properly mourn his father, if the man was to be believed he would need to act quickly to ensure the safety of all of his loved ones. If he was around then they would always be in danger, especially since the NSA and CIA are limiting their protection of him and forcing him to rely solely on Sarah's observations, thus the life of a retiree. He couldn't do that though, not to his family and most of all not to Sarah. Sarah belonged with the agency and thrived on missions and adventure. He had been wrong on the train to assume that she wanted to quit and look how that had turned out. After three days of romantic paradise they were thrust right back into the spy life and they both loved it. Sarah loved it. Sarah loved him. But which would Sarah love the most after one, five, or even ten years? He needed to give her one last choice as to dissuade any doubts his grief stricken mind was having, especially if he was going to pursue his father's enemies. The death of a loved one, the happiness of another, and the safety of the rest were just a few of the thoughts keeping Charles Bartowski from slumber.

At that moment Sarah sleepily rolled away from her position against Chuck's chest and placed her back against him. This temporary reprieve allowed Chuck enough space to roll quietly out of bed and towards the bedroom door. On his way down the hallway Chuck opened the closet door and pulled on four empty coat hangers in quick succession, which opened a compartment in the back of the closet. Grabbing his overnight mission bag that contained spare clothes, equipment and an assortment of non lethal weapons Chuck threw the bag over his shoulder and headed into the living room. Leaving the lights off and moving as stealthily as a Bartowski was capable, he pulled his black mission clothes out of his bag and began to change. He needed to get out for a while and clear his head he decided. Once he was fully dressed Chuck slung the bag over his shoulder and headed for the front door. Before he could reach the door however, movement in his peripheral vision caused him to pause.

_…KERPLUNK…  
_

The stainless steel of the knife glinted in the moonlight as it surreally passed before Chuck's eyes. Chuck very slowly turned his head from the knife sticking out of the wall to his right and then back to the moonlit silhouette of the panty and t-shirt clad Sarah Walker. _Oh boy, I'm going to die. Don't freak out Chuck, play it cool. _Chuck gave himself an inner pep-talk as he turned to face his beautiful girlfriend who was still leaning against the door frame of their bedroom with her arms crossed. _Wow, there's that look again._ Gulp. _What am I going to do?_ Chuck thought.

"Hey Sarah, I'm sorry, did I wake you? I couldn't sleep so I thought maybe I would go out for a little bit."

"You have on your mission gear and it seems you also have your mission bag. You know that I'm not allowed to let non-CIA personnel use CIA equipment. You also promised me that we wouldn't make a decision on anything until after we had a chance to speak to Ellie and everyone else tomorrow morning." Sarah's cool demeanor did not portray the anger and hurt Chuck knew she was feeling. Even though he couldn't really make out all of Sarah's features in the dimly lit hallway he still knew she was giving him _the_ look again.

Sarah slowly made her way down the hallway and towards the front door and a stationary Chuck. "Chuck, do I need to grab my mission bag as well? Since you and I are a team you know we never act alone. I know that you would never act alone Chuck." Sarah reached up and caressed Chuck's cheek with her fingertips.

"You know I've had partners who chose to act without me before, and you know how much they hurt me." Her hand moved to the back of Chuck's head as she leaned in closer.

"You also know that no other partner has ever meant to me a fraction of the amount that you mean to me, I love you Chuck. My entire world resides within this lowly Burbank apartment complex. Now tell me that you aren't acting without me. Tell me that you want to come back to bed with me."

As Sarah drew closer Chuck could clearly see the pain etched in her face.

"I know that you're hurting Chuck and I promise that it will be okay. I will do everything in my power to make it okay." Sarah finally leaned forward and kissed Chuck on the forehead and wiped away the tear tracks now visible in the moonlight.

"Every time I close my eyes, I see him Sarah. I see him falling and not getting back up. If I hadn't made him come back, if I hadn't…" Chuck stopped speaking as Sarah placed a finger over his lips.

"Hush, your father knew the risks, and everything he did, he did for you and Ellie. His sacrifice wasn't in vain, because he gave his life protecting all of ours. Your dad was a great man and American hero; I only wish that I had gotten to know him better. Chuck, your father dedicated his life to protecting you and your sister from afar all while going after the bad people who threaten our world. If that's what you want to do to Chuck, you know I'll be right there with you. But you have to promise me one thing before you do. You have to promise me that we will never act alone, that we are partners and partners always stick together. I can't lose you Chuck, not when I could have been there to keep you safe." Sarah brought her lips to Chuck's and kissed him sweetly as she started to cry. "Promise me Chuck! Promise me that from now on we face everything together!" Sarah cried out and then buried her head into Chuck's chest as the tears began to silently fall down her face.

"I promise Sarah, I promise." Chuck pulled Sarah close to him for the second time that night and took in the sweet scent of her shampoo. Chuck knew that his problems were now Sarah's, even if he wasn't sure how he felt about that yet he knew that he would never betray her trust again. Locked in an impenetrable embrace they both stood there swaying back and forth in the moonlight mourning the loss of Stephen Bartowski.

_**A/N**__ Alright, so what did everyone think? Remember if you liked this chapter please let me know so that I can finish up chapter 2 and get it posted. If you didn't like it than I will just leave this as a one shot. Thanks for the R/R._


End file.
